


Quest to Capture the Shadow Pokemon

by animatedrose



Category: Pocket Monsters SPECIAL | Pokemon Adventures, Pocket Monsters | Pokemon (Anime), Pocket Monsters | Pokemon (Main Video Game Series), Pocket Monsters | Pokemon - All Media Types, Pokemon Colosseum
Genre: Action/Adventure, Corruption, F/M, Friendship, Gen, Guns, Johto mention at start, Orre mention at start, Pokemon snagging, Shadow Pokemon, Shamouti Island, Viridian City, cipher, evil organization bent on world domination, kanto, lots of OCs and character submissions in this, region adventure, rewritten reworked and corrected, this is a rewrite of an old fic on FF.net from 2007-2009, trainer theft
Language: English
Status: In-Progress
Published: 2017-01-02
Updated: 2017-01-23
Packaged: 2018-09-14 08:42:11
Rating: Teen And Up Audiences
Warnings: Graphic Depictions Of Violence, Major Character Death
Chapters: 2
Words: 8,765
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/9171526
Author URL: https://archiveofourown.org/users/animatedrose/pseuds/animatedrose
Summary: The criminal organization Cipher has created Shadow Pokémon to rule the world once again. They have moved from the isolated Orre into the more populated main regions and have expanded their plants to close the hearts of every kind of Pokémon. All they have left to capture is the elusive Legendaries.On a trip to Shamouti Island before his Johto journey begins, Pokémon trainer Mark Hunter encounters a Shadow Pokémon and is rescued by Ho-Oh and Lugia. He is given the duty of capturing all 400+ Shadow Pokémon to stop Cipher from ruling the world! With his Pikachu, Sparks, and the many friends that he meets along the way by his side, can he succeed?BEING REWRITTEN AND FINISHED! THIS IS AN OLD FF.NET FANFICTION OF MINE FROM 2007-2009 THAT I AM ATTEMPTING TO CORRECT AND FINISH THIS YEAR!





	1. The Quest Begins

**Author's Note:**

> So yeah, this thing. My first official Pokémon fanfiction back when I joined Fanfiction.net in 2007. God, this was written so long ago and it’s the only one of my long fics that is even close to being finished (or at least this arc is). I haven’t touched this thing since high school, geez!
> 
> Going back on it, I decided that I at least wanted to finish this. I made it part of my New Year’s Resolution—I’m going to finish these projects. And since Quest started it all, I’m doing that first. 39 chapters to comb through, correct, rewrite, rework, and then (by my estimate) at least three chapters more before this is brought to a close.
> 
> Will I come back to do Johto and such? I’m not sure. My main goal is to at least finish Kanto. If I do come back, cool. If not, I can proudly say I at least brought this section of it to a close.
> 
> Will I expand it to include the other three gens of Pokémon? Not at this time. Sorry but this is staying the way it is right now. If it ever expands, that will be in the way future and I’m not looking that far right now. Sorry.
> 
> So yeah, this is my current NYR project. Expect chapters to be replaced with updated versions. I’m going to try to do this daily and keep it going so I can get to the actual chapter writing ASAP. That will take up the most time. Thankfully, I have my pal and Axl’s creator by my side still to brainstorm out Axl’s whole Champion battle. After that is just Kanto wrap-up and the split between areas for the main crew.
> 
> I hope you all enjoy it, if any one is still watching this dusty old thing.
> 
> Disclaimer: I do not own Pokémon, Pokémon Coliseum, or Pokémon XD. I only own my character, Mark, and his Pokémon team.

   Mark Hunter grinned as he threw a Poké Ball out into the stadium. He was facing off against a trainer in a tournament in Johto. It wasn’t league official, but he took any challenge thrown at him. His Pikachu, Sparks, appeared and faced off against the challenger’s Totodile.

 “Begin!” yelled the announcer, raising his flags.

    Mark smiled and got to work. “Sparks, use Thunderbolt!”

    The Pikachu charged his electricity and fired it at Totodile. It was a critical hit but the water Pokémon wasn’t down yet.

    “Totodile, Water Gun!” yelled the trainer.

    The Totodile blasted water out of its mouth at Sparks, but the Pikachu dodged each blast. He knew what to do next. This was just another run-of-the-mill battle for him.

    “Sparks, use Quick Attack and follow up with Iron Tail!” Mark ordered.

    Sparks ran at the Totodile, who blasted a Water Gun to try and knock him off course. Sparks dodged and leapt into the air, his tail glowing silver. Then Sparks crashed his tail onto the Totodile’s head, knocking it back a few feet. Sparks landed safely on his feet, hours of practice letting him master the technique perfectly.

    “Sparks, finish it off with Volt Tackle!”

    Sparks ran at the Totodile with electricity crackling around his body. The Pikachu collided with Totodile, throwing it back at its trainer and making both fall over.

    “And the winner is Mark Hunter!” the announcer cried, flags waving to signal the end of the match.

    “Good job, buddy,” Mark said as Sparks leaped onto his shoulder.

    The challenger shakily rose, returning his Totodile. “Geez, you weren’t kidding. No wonder you’re one of Prof. Oak’s golden boys.”

    “Uh, I wouldn’t say _that_ ,” Mark said awkwardly, shaking his opponent’s hand. “That might be more accurate if I did more PokeDex filling than battling…”

    “Pika!” Sparks chirped, nuzzling his trainer happily.

    Mark left the pre-gym in triumph, his loyal companion Sparks on his shoulder. Now he felt ready to take on the Gym Leaders here in Johto since he’d gotten a taste of the battling environment. He could already predict that this new journey was going to be a good one.

    But first, he wanted check out that island he’d heard so much about—Shamouti.

    It sounded pretty cool in the brochure and, if he was lucky, he might even see the legendary Kanto birds circling the nearby islands. Even luckier, he might get to see Lugia, though he rather doubted it. Lugia had only been sighted a few times in that area and those had all been during disastrous times.

    But wouldn’t that be just the coolest to see a Legendary Pokémon so early into his new adventure? Talk about a dream come true…

    Mark Hunter walked into the sunlight beyond the pre-gym. He had dark green eyes and green hair with bangs that went in his face sometimes, the rest being bound up in a ponytail that hit his mid-back. He wore a black shirt, a red jacket with black pockets, blue jeans, and black and red tennis shoes. A red bandanna covered his head, letting his bangs poke through to drape over his forehead.

    He walked over to the docks and released his Salamence, a gift he’d received during his Kanto journey months ago. Hopping on the dragon’s back, Mark ordered him to fly to Shamouti Island. The dragon rose into the air and took off for the long flight to Shamouti.

    Roughly an hour later, Salamence landed on the beach of Shamouti Island. Hopping off his back, Mark returned him to his Poké Ball and walked down the beach. He could already see the three islands from here: Ice, Lightning, and Fire Island, where the three legendary Kanto birds lived.

    Shamouti Island was already looking like a good pit stop before his journey began. It was exotic and looked beautiful. The ocean view was fantastic. Mark wondered briefly if there was going to be a festival tonight. He could see a lot of torches further inland.

    Sparks suddenly hopped off his shoulder and ran forward across the sand, cheeks sparking dangerously.

    “Huh? What’s wrong, boy?” Mark asked, confused.

    His gaze followed Sparks until he saw a cluster of rocks further up the beach. Sparks growled, teeth bared at them. Mark tensed. Sparks didn’t just growl at anything. Something was there. Something that Sparks saw as a threat…

    As if summoned, a man with a Raichu came out from behind the rock cluster. He had on all black clothes and had red hair peeking out from beneath a wide brimmed hat. His eyes were hidden by dark sunglasses.

    He had to be a trainer of some kind, judging by the presence of the Raichu…but something about him was bugging Mark. Something bad. What was it?

    The man smirked and pointed at them. “Okay, kid, make this easy and hand over that Pikachu.”

    “What?” Mark replied, alarmed. “Why should I? Why do you want Sparks?”

    “None of your business, kid!” snarled the man. “Raichu, use Shadow Bolt on that kid and take his Pikachu!”

   The Raichu stepped forward menacingly. Its cheeks sparked and it released a powerful Thunderbolt. Mark yelped, realizing that the blow was aimed at him. Sparks instantly countered with a Thunderbolt, saving Mark from getting hurt.

    “So you wanna fight back now, huh?” taunted the man. “Well, if it’s a battle you want, it’s a battle you’ll get! Raichu, use Shadow Bolt and then Shadow Rush!”

    Mark stepped back, trusting Sparks to be able to handle this. His mind was a whirl of confusion. The attacks that the man shouted made no sense. Those weren’t moves that Mark recognized at all. Were those new?

    And the Raichu itself…

    Something about it was all wrong, but Mark couldn’t identify what exactly it was. Its attacks were too powerful. He’d battled plenty of Raichu before and none of them could compare to this one. Did this guy—clearly some kind of Pokémon thief—illegally buff up his Raichu somehow? He didn’t look like he was part of Team Rocket. Maybe some other organization? Mark couldn’t see any identifying gang symbols on him.

    The Raichu let out another explosive Thunderbolt that was countered by Sparks’ own Thunderbolt. Then Raichu tackled Sparks to the ground, using its bulk to try and crush him. Sparks cried out, clawing at the larger mouse in a bid to keep from being flattened.

    “Sparks, break away and use Quick Attack!” Mark called.

    Sparks growled, twisting to bite at the Raichu’s nearest paw. The larger mouse screeched, rearing back in pain. Sparks quickly leaped away and sped around the larger Pokémon, taking advantage of the other’s weakness to try and scope out weak points on it. Then Sparks hit the Raichu with a Thunderbolt to its back. The Raichu hissed, whirling to face him in just the nick of time to block the Thunderbolt with its own attack. It struck again right afterward and hit Sparks directly, throwing the Pikachu back a few feet to roll across the sand.

    “Sparks, use Iron Tail!” Mark ordered, growing frantic. He could see that his Pikachu was taking a beating out there.

    Sparks got to his feet and ran at Raichu, leaping into the air as his tail started to glow silver again. But Raichu would not wait for Sparks to be ready.

    It pounced, ramming into the airborne Pikachu to knock Sparks back to the sandy ground. Raichu then tackled Sparks again and hit him with a close-range. Sparks fell back and tried to get up, but Raichu rammed him again. The winded and aching Pikachu collapsed at Mark’s feet.

    “Sparks!” cried Mark as he dropped to his knees and grabbed Sparks, holding him close.

    Laughter tore his attention away from his Pikachu.

    “Told you, kid!” laughed the man, walking over to him with the Raichu following. “You should’ve just handed over the Pikachu and you could’ve saved me the trouble of beating it senseless first. Kids these days!”

    “What do you want with Sparks?” Mark asked, eyeing the Raichu suspiciously. “To turn him into what that Raichu is?”

    The man grinned and pulled out a gun. Mark flinched instantly. It wasn’t that the sight of a gun was so shocking. Guns were just as prevalent in the world as Pokémon were. It was the sight of a trainer making use of one that was surprising. Most gangsters and evil organizations never bothered with guns because they used Pokémon for their dirty work.

    This guy—and whoever else may be with him—clearly preferred to use both to get their job done.

    “Precisely,” the man said. “We’ll turn that Pikachu into a Shadow Pokémon.”

    “Shadow…Pokémon?” Mark repeated.

    The term didn’t sound familiar. Was that a new kind of Pokémon? Clearly it was an artificially engineered one, if Mark had to guess. No regularly raised Raichu could be that immensely strong.

    It made him worry about what could happen to Sparks if such a thing was done to him.

    “That’s right. Pokémon who have had their hearts closed,” the man said smugly, passing the gun between his hands idly. “They have an advantage against all Pokémon and their attacks are effective against all types. They’re even resistant to their own type, which is the reason your Pikachu couldn’t beat my Raichu. They’re the ultimate tools for world domination on a scale that no other group could ever hope to reach.”

    Mark felt the cool metal of the gun against his forehead. The man wouldn’t stop smiling down at him.

    “There’s one Shadow Pokémon of each species in the PokeDex, except for the legendaries…for now. Master’s working on that,” the man said, smirking. “Soon we’ll have the whole world bowing to us. To Cipher!”

    “Then why do you need Sparks? Don’t you already have a Shadow Pikachu?” Mark asked, looking at the weakened Pikachu in his arms.

    He filed the information he was hearing away. If he survived this, he’d need to get this to the police pronto. Whatever this Cipher group was, they were seriously bad news.

    “Yeah, we do. But I could always use another Pikachu as fodder.” The gun was pressed firmly against Mark’s forehead now. “And now that you know all of this, I’ll have to kill you. Say good bye, brat!”

    The man’s fingers started pulling the trigger. Mark tensed. So much for running to the police…

    A loud shriek tore through the air and a blast of fire crashed into the ground near them. The man jumped back, head snapping toward the sky, while Mark stayed there in shock. Circling above them, letting off Sacred Fires and Aeroblasts, were two of the most iconic Pokémon in all of Johto—Ho-Oh and Lugia.

    All of these attacks were clearly aimed at the man, not Mark. He had his Raichu defend him with bursts of lightning, but it was tiring quickly. Sparks had managed to do enough damage to it during their fight. And up against two Legendaries, even a beefed-up Raichu couldn’t win.

    “Pi…ka…” Sparks squeaked.

    “Sparks, you’ll be okay,” Mark said, fumbling for his Poké Ball. “I’ll get you to the village. There’s gotta be one here. Somebody can help you.”

    “Pi…” Sparks shook his head and tried to crawl off of his trainer’s lap, a paw extending past Mark’s knees. “Pika!”

    “Huh? What are you…? What the heck?”

    Mark looked where Sparks pointed and noticed a necklace was lying in the sand in front of him. It clearly hadn’t been there before, if Mark’s memory was right. It was a small black ball the size of his thumbnail with a silver feather bordering one side of it and a rainbow feather on the other. It was on a gold and silver chain. It was certainly beautiful.

    Mark shuddered. He had a weird feeling about this necklace. Some inner voice spoke to him, telling him that this was his. Though nervous, Mark grabbed it and carefully put it around his neck.

    As soon as he did, he looked at the scene before him and saw that something was different.

    The Raichu! It didn’t look normal at all.

    Its coloring was all wrong. Instead of having brown paws, they were black. Instead of having a yellow cheeks and lightning-bolt tail, they were red. And its eyes were glowing red, like nothing Mark had ever seen before.

    The real kicker was its aura. The Raichu looked like it had a cloud of shadow wreathing it. It was a wispy purple-black cloud that swirled and clung to the large mouse’s form, accenting its darker colors. Mark could suddenly understand why it was called a Shadow Pokémon now.

    When he carefully took the necklace off, the Raichu looked normal again.

    Putting it back on, he felt warmth coming from the necklace. He looked down and saw it was glowing vibrantly. With a squeak, Sparks suddenly rose without difficulty. The Pikachu’s injuries were healing!

    Mark then realized what was going on.

    The feathers on the necklace! They were Ho-oh and Lugia’s feathers. That’s what had to be healing Sparks.

    Which meant that the black bead at the center…was what was letting him see these strange Shadow Pokémon in their real forms.

    Standing back up, Sparks jumped out of his arms. Lugia and Ho-oh disappeared abruptly into the clouds, leaving the man and his Raichu alone. Sharp clicking signaled that the gun had been emptied of its bullets during the panic.

    “You! You did that, didn’t you? Calling Legendaries on me! You pesky brat!” the man accused wildly. “Raichu! End this kid!”

    His Raichu immediately launched a Thunderbolt—no, a Shadow Bolt, Mark could now see the darkness that coated the lightning and made it so explosive—at Sparks, who easily dodged it. Mark wasn’t sure if Sparks could see it to or if the Pikachu was falling more on instinct to evade being hit. Whatever it was, it was working.

    “Sparks, use Iron Tail and follow up with Thunderbolt!” Mark yelled.

    Sparks leaped into the air and smashed his glowing tail down on Raichu’s head. Hopping a safe distance away, the Pikachu used Thunderbolt on Raichu. An explosion ensued and, when the smoke cleared, the heavily weakened Raichu was down, struggling to rise.

    The man went crazy, shouting and yanking his hair. He turned, racing away across the sand in a mix of rage and terror. “How could a kid beat me and my Shadow Pokémon?! You remember this, kid! Cipher will be after you for this! Remember!”

    Mark watched him run, not sure if he should pursue or not. He decided against it. Though empty, the man still had a gun. It was probably best to clear out now before that guy came back.

    That left the man’s Raichu, lying in the sand, alone and injured.

    “Weird. Did he abandon his Pokemon?” Mark asked, looking down at the Raichu in pity. “For a guy who claimed his organization only had one of you, he sure was fast to ditch you.”

    He couldn’t just leave it lying there. What if it died? And it was foolproof evidence of what this Cipher organization was doing. He had to take it to the police.

    But how?

    Another feeling washed over him. It had to be coming from the necklace. It told him to catch it. But…that was impossible. You couldn’t catch other trainers’ Pokémon! It was against the law!

    Then again, he had no proof that that man had caught this Raichu at all. It was worth at least checking, right?

    Mark sighed and grabbed a Poké Ball, tapping it against the Raichu’s limp frame. The Poké Ball opened and the Raichu disappeared in a flash of red light.

   “I guess he didn’t catch it?” Mark muttered.

    He still felt bad about this. The Raichu wasn’t his. He shouldn’t be catching it. What if the police decided he was a thief?

    Mark picked up the Poké Ball and jumped when it suddenly began to change. The red part darkened to black and the white part became gray. A jagged red ‘S’ appeared on the black part, right above the button. It was like an entirely different kind of Poké Ball now.

    He’d never seen a Poke Ball like this before. Was this also related to the necklace?

    Was the Raichu inside still okay?

    “Uh… Come out, Raichu,” Mark said, opening the Poké Ball.

    The Raichu popped out, still injured but conscious. It swayed slowly on its long feet, looking dazed. Mark sighed in sadness and picked it up in his arms.

    The Raichu suddenly smirked and shocked him with a blast of shadowy electricity.

    Mark cried in shocked, instantly tensing for the pain…and then realized that he felt nothing. The attack…wasn’t working?

    His chest felt warm. The necklace was glowing white and the attack faded from existence. The Raichu was confused and fell limp in Mark’s arms, burying its face into his black shirt. It looked angry and ashamed.

    Mark breathed a sigh of relief. Sparks used to electrocute him a lot back when he was a beginner. He knew what electricity felt like. He was glad that he was able to avoid this buffed-up version of a standard Thunderbolt.

    A loud shriek was heard overhead.

    Mark jolted, looking up to see Ho-oh heading right for him. He yelped, racing further inland to avoid becoming a landing pad. Ho-Oh landed lightly in front of him, rainbow wings folding elegantly against its large frame. Lugia landed beside the Ho-Oh and glanced at the Raichu, a troubled look on its draconic face.

    Then the Ho-Oh spoke.

    “Get on.”

    Mark was confused. “What? Why?!”

    He’d heard of the telepathic abilities of Legendary Pokémon. It was popular in myths and stories, but never having run into a Legendary before, Mark had been iffy about that. Now he knew for sure. It was actually quiet terrifying.

 Sparks darted away from him, running up Ho-Oh’s wing and resting on its shoulders just behind its neck. “Pika pi!” he cried, waving a paw as if to invite his trainer to join him.

    “You will not be harmed, but we need to speak with you,” Lugia stated. “Get on.”

    Mark sighed in defeat. This was a losing argument, that much he recognized. He walked over to the Ho-Oh, climbing onto its back when the birds lowered itself. He sat behind Sparks, gripping the rainbow feathers with one hand while his free arm wrapped around the Raichu huddled against his chest.

    “Hang on,” Ho-Oh said.

    Then Ho-Oh took off with a monstrous flap of its wings. Mark clung to the feathers on its neck while Raichu clung to his shirt. Sparks hung onto the feathers too. Soon the two Legendaries were flying high over the ocean, flying away from Shamouti and its surrounding islands.

    “So, you wanted to talk. If you know anything, I at least want to know why that man attacked me,” Mark said, hoping that they had the answers.

    “Just as he stated: to have another Pokémon to mess with,” Ho-Oh replied.

    “Well…” Mark started, glancing at the Raichu clinging to his shirt. “Who is Cipher? And what are they doing to make Pokémon into…Shadow Pokémon? What _are_ Shadow Pokémon, anyway?”

    “Cipher is an evil organization dedicated to closing Pokémon’s hearts and turning them into battle machines,” Lugia responded, tone cold and bitter. “They’ve done this twice before in the past, in a far away region called Orre, and failed. Now they’re doing it again, moving from the isolated Orre into more populated regions to expand their reach.”

    Mark frowned. He’d never heard of a place called Orre before. He made a note to look for it on the next world map he saw.

    “Shadow Pokémon are unusual. With their hearts closed, they’ve become violent creatures whose sole purpose in life is to fight and win by any means necessary,” Ho-Oh said, sadness in its voice. “All of its original moves are forgotten and replaced with Shadow moves, bypassing all type advantages to equally hurt any Pokémon that opposes it. They can’t level up, evolve, or learn any new moves beyond the ones Cipher has implanted in them. These moves can even cause the Shadow Pokémon to possibly hurt themselves in battle.”

    “Cipher has implemented their plan by expanding their own numbers. They have corrupted over four hundred Pokémon with their cruel science,” Lugia said. “I have witnessed their acts with my own eyes. They must be stopped at once before they consume the entirety of the planet. But we Legendaries can only do so much. We ourselves are at risk for capture by Cipher now. That is where you, human, come in.”

“Wait! Me? Why me?” Mark asked. “Why are you telling me all of this? I may have caught this Raichu, but I can’t catch over four hundred Pokémon! That’s insane! You need to tell the police or something! Really strong trainers!”

    “We don’t have that much time, human! You’ll have to do for the moment. If you wish to inform your governments, then do so,” Lugia said. “But right now, you are all we have. Your mission is to save the Shadow Pokémon from Cipher’s evil clutches and purify them. You must steal back the ones who are being abused by criminals and open their hearts again. Anyone else who sees them won’t know they are Shadow Pokémon. Only you can see them, human.”

    “But how?” Mark asked, confused and overwhelmed by the task set before him. “How do I stop Cipher? How do I purify the Shadow Pokémon? You aren’t telling me everything!”

    “That,” Ho-Oh said as they flew lower. “You will have to discover on your own, human. Use the Snag Balls to capture them and then find a way to purify them. If you open their hearts, they will be free from Cipher’s influence!”

    Mark groaned, suddenly feeling queasy. This whole mission sounded like a big pot of trouble. Did he really want to get involved in this? He just wanted to journey around Johto with his team and have some more fun.

    Mark looked down past Ho-Oh’s wing and saw none other than Kanto below them. That made him jolt. What were they doing here? He’d gone to Johto to get away from Kanto for a while!

    “Why did you bring me here?” he demanded, unfairness welling in his chest.

    “We sense many Shadow Pokémon residing here,” said Lugia. “You must find them and catch them. We can do no more for you now, human.”

    “Wait, you’re just leaving m—AAAAAAAAHHHHHHHH!”

    Ho-Oh abruptly swung its body sideways, throwing Mark off and sending him falling into open air. Sparks cried out, flapping his paws frantically. Mark stared up at the circling Legendaries in shock and betrayal.

    “Good luck, human!” the two Legendaries cried.

 

.o.o.o.o.

 

 Mark landed in a huge pile of hay. It wasn’t the most comfortable landing ever, but it beat hitting the ground. Looking up gave him no sign of either Johto Legendary. He was alone in a hay field with his Pikachu and a battered Raichu.

    “Oof! Nice landing, eh?” Mark grumbled. “What were they thinking, letting me fall a couple hundred feet in the air? They’re lucky I landed here! Right, Sparks?”

    His Pikachu nodded, flopping onto his chest. The Raichu was by his side, breathing heavily from the sudden drop. Mark sighed and returned it to its Poké Ball—a Snag Ball, as Ho-Oh had called it. Putting it on his belt, he slid down the hay pile with Sparks.

    After picking the hay out of his hair and clothes, Mark looked towards where the sun was setting. Sparks pounced on his jacket and grabbed at a thin rectangular object sticking from his pocket. It tumbled to the ground.

    “What’s that, Sparks?” Mark asked. He didn’t recalling having anything in his pockets.

    “Pika pi!” Sparks said with a look that said ‘How should I know?’

    “Hey,” said Mark, picking it up. “I know what this is! This is a PDA, a Pokemon Digital Assistant! This thing stores massive amounts of data and holds a ton of personal information on it. But these are expensive as heck! How did I get one?”

    He turned it on. It worked just fine. It wasn’t registered to a user, so it was clearly new. He checked the menu screen and saw something that he’d never seen before.

   “A Shadow Monitor? What’s that?”

    Mark turned the application on. A bunch of lists and windows popped up. After doing some sifting around, Mark felt elated. The Shadow Monitor had a list of all the Shadow Pokémon, showed who they were being carried by, and where they were at the moment.

    “Awesome!” Mark cried in joy.

    “Pikachu?” squeaked Sparks, looking confused at his trainer’s happy face.

    “Sorry, Sparks, it’s just that…” Mark grinned, petting Sparks’ head. “It’s just that with this thing, everything is a lot easier. I know where they are, their level, attacks, trainer, everything! I can actually preplan some of this stuff! Maybe this won’t be so hard after all…”

    “Pika pi! Pikachu!” Sparks cried, leaping on his shoulder.

    “Alright then, Sparks! Let’s go catch some Shadow Pokémon!” Mark said, walking along a path through the field of hay piles. “But first…”

    He picked up Raichu’s Snag Ball and looked it over. He knew it was essentially forbidden to capture another trainer’s Pokemon, but the criminals using the Shadow Pokémon were leaving him no choice. And it was for the good of the Pokémon, right?

    Surely the police, and anyone else who saw him doing this, wouldn’t be mad. He was doing a good thing, right? This was saving innocent Pokémon. It had to be okay.

    Half an hour of walking led him to finding a city. It wasn’t very big. It was even familiar. Mark entered the Pokémon Center, which informed him that he was in—where else?—Viridian City.

    It was like starting his Pokemon journey all over again but, instead of catching normal Pokémon, he was catching Shadow Pokémon and trying to stop some evil organization intent on complete world domination.

   Mark rented a room for the night in order to rest. Hopping into bed, Sparks fell asleep instantly. Mark, on the other hand, stayed awake for a few more hours, trying to figure out how this was all going to work.

    Should he really go to the police? Should he backtrack to Pallet Town and find Prof. Oak? Tell a Gym Leader? Or should he forge ahead and try doing this alone?

    When 2AM rolled around, Mark ended up falling asleep with thoughts of how to purify Raichu. His dreams seemed to say that his PDA would tell him how to purify them, but how truthful were dreams? Maybe it did, but he’d have to figure it out in the morning. Right now, Mark needed sleep more than anything else.

    That night, his dreams were filled with claws, fangs, blood, shadows, and screams. It was not a pleasant sleep.


	2. Rocky Starts

**Notes for the Chapter:**

> Here we go with chapter two of this rewrite. Feeling good so far.

    Mark woke up the next morning to Sparks smacking his cheek insistently. The sunlight poured through the open window to light up the room. The green-haired boy groaned before slowly sitting up.

    “Morning already?” he yawned.

    “Pika!” Sparks chirped, leaping off of the bed and bounding for the door. “Pika pi!”

   “Yeah, yeah, I’m coming. I’m hungry too, you know,” Mark muttered.

    The trainer dragged himself out of bed and left the room with Sparks at his heels. The breakfast room downstairs held only a few other trainers in it. Mark made himself some toast for breakfast and grabbed some PokéChow, making his way back upstairs to his room. His Pokémon were better off being fed here than downstairs, especially his newest catch.

    Setting out the individual bowls of food, Mark watched Sparks dig in eagerly before releasing the rest of his Pokémon: his Salamence, the Mightyena that he’d been given from a friend in Hoenn, and the Shadow Raichu that he had caught yesterday on Shamouti Island.

    Seeing that Raichu was what reminded Mark of his mission. It cemented the fact that this was not a dream. That he’d been pulled from his planned Johto journey, transplanted back into Kanto by Lugia and Ho-Oh. That he had a very big job ahead of him.

    And he had no clue what to do in terms of purifying any of the effected Pokémon.

    Recalling his dream, he checked his PDA for answers about purifying the Raichu but there were no known ways listed in it. He reluctantly admitted that Ho-Oh was right. He’d have to figure it out on his own.

    Maybe he could look up Cipher on his PDA and see if any ways were listed there? It was worth a look.

   He checked. None. Mark sighed, head hung in defeat.

    “That was pointless,” he grumbled, finishing his toast.

    He felt a tugging sensation on the leg of his jeans. Mark looked down to see the Raichu doing the tugging. Mark still thought it looked creepy with the red eyes and the black paws, so very different from the typical Raichu.

    It looked confused. Maybe frustrated? Mark wasn’t quite sure since its facial expression always seemed on the negative side of the emotional spectrum.

    “Rai? Rai rai chu?” it squeaked, continuing to tug his jeans.

    “What is it, Raichu?” Mark asked, stroking its head in what he hoped was a pacifying manner.

    The Raichu instantly growled and bit his hand, its fangs drawing blood.

    “Ouch!” Mark cried, yanking his hand free with such force that he fell out of his chair. “What was that for?”

    “Rai raichu!” the Raichu cried, waving its arms in obvious frustration. “Raichu! Rai! Chu!”

    “I don’t understand, Raichu. What do you want?” Mark asked, concerned and a smidge afraid of its sudden change in behavior.

    Mark looked at Sparks, who only shook his head. The Pikachu abandoned his food dish to approach the larger mouse, talking to the Shadow Raichu in its own language. This only lasted a minute before, in a fit of anger, the Raichu shocked Sparks and tackled him to the ground. A brief tussle ensued across the carpet flooring of the room, both Pokémon squeaking and scratching at each other.

    “Guys! Knock it off!” Mark ordered.

    He was ignored entirely by the two Electric-types. Salamence watched the fight with mild disinterest, more concerned with devouring his bowl and then stealing from Spark’s half empty bowl. Mightyena, angered by the duo’s refusal to obey her trainer, ended up rising from her place to stop the fight with a very loud bark.

    “Ow! Good job, girl,” Mark said, rubbing his ringing ears. Sometimes he forgot how loud his Mightyena’s bark could get. “Good job.”

    Mightyena barked and returned to her bowl of food, eating quickly. Salamence downed the last of Sparks’ food before resting on the carpet, taking up most of the floor. Mark returned him after a moment, not wanting to trip over the dragon.

    Raichu glared at Mightyena, clearly bitter about her ending the scuffle that it had caused. Mightyena pointedly ignored it, as was her nature. Sparks licked his wounds, some of the scratches having cut his skin, leaving faint patches of red on his yellow fur. They weren’t very bad, thankfully.

    Mark looked through his PDA again once the fuss had died down. It had a Shadow Pokémon Pokédex in it, so maybe it could tell him what was wrong with Raichu? Again, it was worth a look.

    The screen displayed Shadow Raichu’s PokéDex entry, looking no different than a standard PokéDex entry. There was a tiny addition, though. There was frowning face emoticon above the image of the Raichu.

    “You’re upset? Why? Because my Mightyena made you quit attacking Sparks?” Mark asked, baffled. “If that’s it, get used to it. I’m not letting you take your anger out on my Pikachu just because you think you can.”

    Raichu bristled and gave a cry before tackling Sparks. The two electric mice rolled along the floor again, scratching and biting. Mightyena rose with a snarl, fangs bared, only for Sparks to squeak loudly at her. Mightyena paused before she settled back again, though she watched warily.

    Sparks and the Shadow Raichu parted moments later, the latter’s cheeks sparking viciously. Sparks gave a squeak and looked at Mark.

    “…He wants to battle?” Mark guessed.

    It was really the only thing he could guess. Why else would Raichu keep attacking Sparks? Clearly it wanted to do what Cipher created it to do—fight.

    Shadow Raichu gave a cry of triumph. Sparks nodded, smiling at him.

    Mark sighed in relief. At least he knew what was wrong.

    But now a new worry gnawed at him. This Raichu had proven itself to be very dangerous. Was it even safe to let it battle? It seriously hurt Sparks back on Shamouti Island. If it did that during a battle with another person…

    “Pika?” Sparks prompted.

    “…I don’t know,” Mark admitted. “If someone sees it…”

    “Rai? Raichu rai!” Shadow Raichu cried, butting in on the conversation.

    “I just don’t think that’s a good idea right this second. Sorry,” Mark apologized.

    “Rai…?” Shadow Raichu turned back to its food bowl, looking angry and rejected.

    It made the trainer feel bad…but he had to think about the safety of others, too. Until he knew more about this Raichu, it probably wasn’t a safe bet to jump right into battle.

    Mark looked at its PokéDex entry again, just to gain some necessary facts about the Shadow Pokémon. Better safe than sorry.

    The Raichu seemed normal besides the color changing, but its stats were off a little. It was speedier than a normal Raichu and had a high Attack stat. It looked like Cipher messed with its stats to make it quicker and more aggressive.

    He easily found the basic facts: it was male, had the normal Static ability, and was at Level 18. Cipher must have turned him into a Shadow Pokémon as soon as he leveled up and evolved with a Thunderstone. His attacks were Shadow Bolt and Shadow Rush.

    After breakfast, Mark checked out of the Pokémon Center and left. Sparks was on his shoulder and the PDA was in his hand, the Shadow Monitor activated.

    According to the PDA, there was another Shadow Pokémon in the woods near the city. It was a Shadow Espeon. Mark followed the monitor until he reached the edge of a clearing. Standing there was a boy with blue hair. Mark entered the clearing with his shoulders hunched, PDA shoved into his jacket pocket.

    “Oh! Hello there,” the boy greeted. “I didn’t think anyone would find me out here!”

    “Hey,” Mark greeted.

    This kid didn’t look dangerous. He couldn’t be much older than Mark was, maybe a year younger. Would Cipher actually recruit random kids to handle these dangerous Shadow Pokémon?

    “Hey, are you up for a battle?” the kid asked. “I just got this really strong Pokémon and I’m dying to try it out on someone! Interested?”

    This could be it—his opportunity to see if this really was a Shadow Pokémon or not.

    Mark smiled in a welcoming way. “Sure! Sparks, are you up for this?”

    “Pika!” Sparks cried, bounding across the grass.

    “Sweet! Let’s do this!” the boy cried, tossing a Poké Ball.

    It was a Nidorino, unfortunately not the Shadow Pokémon that Mark was looking for. He fought to hide his disappointment.

    “Nidorino, Horn Drill!”

    “Sparks, use Thunderbolt!”

    Sparks ran at it and unleashed the burst of electricity, stunning the Nidorino. Another burst of lightning forced it down, defeated. The boy returned it and threw out a Beedrill next. It also wasn’t the Shadow Pokémon.

    “Beedrill, use Twinneedle now!”

    The wasp Pokémon flew down and struck Sparks hard with its needles. The Pikachu stumbled back, side aching, but he got up and shot out another Thunderbolt, easily knocking it out. The boy gritted his teeth in frustration and returned it, throwing out his final Pokémon.

    “Espeon, go!”

    The instant it emerged, Mark knew. This was it. This was the Shadow Pokémon that his Shadow Monitor had summoned him for.

    The Espeon’s fur was a deep shade of red, contrasting with the red glow of its eyes and the darkness of the jewel on its forehead. A dark aura billowed around it like smoke. It was terrifying to look at.

    “Where did you get that Pokémon?” Mark demanded.

    “From some guy in a black robe after I beat Brock. Why?” the blue-haired trainer asked.

    “That’s a Shadow Pokémon!”

    Mark’s heart stopped when the kid smiled. It was menacing.

    “So what? Does that honestly matter?”

    “O-Of course it matters! Do you have any idea what has happened to that Pokémon?” Mark barked, angered by the nonchalance that this kid was showing.

    “Not really. All I know is that it’s supposed to be super strong. I’ve beaten everything in this area already. Now I’ll beat you,” the kid said.

    “If you want to keep battling, then bring it on!” Mark growled. “I’m taking that Espeon from you!”

    “Taking it? Just try!” the kid challenged, grinning widely. “Espeon, use Shadow Hold and then Shadow Panic!”

    The Espeon’s jewel glinted darkly, beginning to glow. A black aura descended around them, wispy and billowing like what poured from a Shadow Pokémon’s body. Mark shuddered, the hairs on his arms standing on end. It was like being in a mist, but much darker and malevolent.

    Then the aura started pulsing around them, as if it were a living thing. There was a strange noise in the air, like the buzzing that one got in their ears.

    Sparks looked around wildly to find the noise, alarmed. Mark struggled to stay calm, fear suddenly welling in his chest. If he panicked, then Sparks would stand no chance. He needed to keep his cool and defeat this guy as fast as possible.

    It was hard, though. The fear seemed to swallow him whole.

    “Sparks, use Thunderbolt!” Mark commanded, voice shaking.

    Sparks trembled, charged with electrical energy. The Pikachu bristled and shot out the attack…but the bolt arced backward, striking Mark head-on. The boy cried out at the brief burn before the attack dissipated, leaving his hair singed and his throat and nostrils burning. His limbs tingled, bordering numb and agonized.

    “Ugh… Sparks! You…attacked me?” Mark choked.

    That wasn’t right. Sparks hadn’t attacked him since they started journeying together in Kanto. Once Sparks had gotten control over his electricity, the stray shocks stopped happening. He hadn’t been electrocuted by his friend in a few years.

    “Confused?” the blue-haired boy asked, smirking. “Shadow Panic causes your Pokémon to be confused.”

    Okay, that made sense. So Sparks hadn’t done it by choice. Mark struggled to shake off the tingling in his limbs. The Pikachu stumbled, trying to shake off the confusion he was afflicted with.

    “Now Espeon, use Shadow Rush!” the kid ordered.

    The Espeon raced forward and tackled Sparks, throwing him back along the grass. The dark aura dissolved from around them. Not that it helped much now. Sparks was knocked out, confusion and the Espeon’s attack doing him in.

   _Oh man_ , thought Mark, looking at the Espeon. _This is bad. This guy might actually be on a whole other level!_

    Something bumped his hip. Raichu’s Snag Ball had started to shake violently. Mark unhooked it warily, yet the expected shock didn’t come.

    An idea suddenly hit him. _Does Raichu still want to fight?_

    “Okay then, Raichu! Come on out!” Mark yelled, throwing the Snag Ball.

    Raichu popped out, blinking at the sudden shift in light. Once he recovered, the rodent looked up to see Espeon. Raichu bristled, instantly looking ready to fight.

    “Okay, Raichu, use Shadow Bolt!” Mark ordered.

    Raichu didn’t hesitate. He even seemed eager as he charged up the attack and shot it at Espeon. The fox tried to dodge but the bolt, as if commanded telepathically by Raichu, arced and struck it anyway. It cried out as it was engulfed in black lightning.

    Once the lightning dissipated, the Espeon collapsed, unable to rise. The boy stared in shock.

    “N-No way. I was told that it was super strong,” he babbled. “That nothing could beat it. No way!”

    Mark pulled a Poké Ball from his belt, weighed it in his hand momentarily, and then finally threw it at the Espeon. The boy yelped, jumping back. He gave a shout when the Espeon was sucked into the Poké Ball, pinging to signal a successful capture.

    Mark picked up the Poké Ball, a small smile on his face. _I guess capturing them works, even if they are captured by another trainer. There’s that worry out of the way._

    The Poké Ball turned into a Snag Ball in his hands, just like Raichu’s did. Mark pondered briefly at the coincidence of that. Was his touch required for the change? How did it know that it was him touching it? Maybe the necklace was involved somehow?

    The blue-haired boy was gone when Mark looked up. The kid had probably taken off once he realized that his Espeon was truly gone, that Mark had kept his promise to take it from him. Hopefully the kid couldn’t properly ID him if he ran to the police.

    Mark sighed, leaving the woods and returning to the Pokémon Center. He contemplated renting a room for a few nights. It could be helpful since the Shadow Pokémon kept tiring his Pokémon, and thus him, out.

    He decided that was indeed the best course of action for now.

    After renting a room and getting his Pokémon healed, Mark collapsed on the bed. His feet ached from all the walking. He pulled out his PDA, deciding to check Shadow Espeon’s stats and information while he was laying there.

    It was female, had the normal Synchronize ability, and was Level 16.

    Mark noted that she had gone down a lot quicker than Raichu had on Shamouti Island. She wasn’t very fast and, so far, both of them had rather poor Defense. Why? What was Cipher’s goal in that?

    Mark’s stomach growled, alerting him to the time—time to eat, that is. After fixing up some sandwiches for lunch from the food downstairs in the dining area of the Pokémon Center, he let out his Pokémon again. The Shadow Espeon stared at the PokéChow while the others ate. Even Raichu seemed more eager to eat now, sated by the brief fight with Espeon.

    “What’s wrong?” Mark asked, noticing her lack of movement. “Aren’t you hungry?”

    The Espeon looked at him, blinking her glowing red eyes slowly. _Where is my owner?_ she asked telepathically.

    “That kid was a criminal, Espeon,” Mark explained, not bothering to beat around the bush. “He was helping an organization called Cipher, who closed your heart. For all I know, he helped turn you into a ruthless fighting machine. My job, as appointed by Lugia and Ho-Oh, is to find out how to open your heart again and set you free.”

   _You sound uncertain as to how to do this,_ she noted.

    “Hey! I’m still learning. I only got dragged into this yesterday,” Mark grumbled.

   _Then why get involved at all? I am not in pain. There is nothing wrong with me,_ Espeon said.

    “Because you don’t deserve to be used like a machine. No Pokémon does! You shouldn’t be attacking people the way that guy tried to make you do. Like what you made Sparks do,” Mark explained, glancing at his Pikachu. “That’s not how people or Pokémon should react to each other. We’re supposed to be friends, equals even. I know I don’t know how yet…but I want to try and find a way to get you back to normal.”

    … _And if you cannot?_ Espeon challenged, eyes narrowed.

    “Then I can’t. I’ll just find someone who can in my place,” Mark declared, arms crossed over his chest. “Now then…are you going to eat? Or keep giving me pop quizzes on stuff that I don’t know? Because if you don’t eat soon, my Salamence will end up eating your food.”

    The Espeon bristled and turned to her food, quickly meeting gazes with the Salamence. He withdrew, instead eyeing Sparks’ bowl. The Pikachu hovered over his dish in silent challenge. The dragon huffed and proceeded to lounge on the floor in defeat.

    Eating slowly, the Espeon watched Raichu. If what she sensed was true, he too was a Shadow Pokémon. He was like her, a Pokémon with its heart closed, as Mark explained it.

    Raichu seemed relatively happy. A bit frustrated, charged with energy. Ready to fight again, to take on another opponent. Besides that, he did not seem too terribly upset to be here.

    Maybe it wouldn’t be so bad, being Mark’s Pokémon now.

    Mark smiled, noticing Espeon’s relaxed posture. He now had five Pokémon, including two that were Shadow Pokémon. Two down, over four hundred to go.

    This was getting fun, in his opinion. All he was doing was battling. He lived for battling. He just hoped the Pokémon weren’t all as unruly as Raichu was at first.

    Shortly after lunch, Mark felt the Shadow Monitor go off. Another Shadow Pokémon was nearby. It was close to where he had landed in the hay field yesterday.

    Grabbing his bag and returning everyone but Sparks, he ran out of the Pokémon Center and down the road out of Viridian City. The hay field was roughly between Viridian City and Pallet Town, if he guessed correctly. If that Shadow Pokémon got into Pallet Town…

    Reaching the hay field, Mark held his monitor up in search of the trainer that was supposedly here. It didn’t take long to find her. Close to the fence on the far side of the field was a girl with short light blue hair. She smiled when he approached, noting the PDA that he shoved into his pocket.

    “Ooh! Are you a trainer?” she asked. “Oh, you must be! You have a Pikachu on your shoulder!”

    “Yeah, I am,” Mark admitted. “Why? Looking for a battle?”

    “Oh, you bet! I like to follow the meet-eyes-and-battle rule!” she chirped, pulling out a Poké Ball. “Plus I get to test out my new Pokémon!”

    Mark nodded, throwing Mightyena out. “A new Pokémon? That should be fun. Let’s go!”

    “Sweet!” said the girl, throwing out an Azumarill. “Let’s do this! Azumarill, Bubblebeam!”

    “Mightyena, Bite!”

    Azumarill blew bubbles rapidly out of its mouth, punching into the ground wherever they struck. Mightyena dodged most of them and lunged when she saw an opening, biting Azumarill hard on an ear. A few swift shakes made the water mouse faint.

    “Oh no! You big meanie!” she cried, returning it. “You’ll pay now! Go, Umbreon!”

    When the Umbreon popped out, Mark knew instantly that this was the Shadow Pokémon that he had been looking for. It was still black but the yellow bands had turned red to match its glowing red eyes.

    “Finally! I was hoping that it was you that had it!” said Mark. “Mightyena, Shadow Ball!”

    Mightyena growled, jaws parting to shoot a huge black ball of energy out of her mouth. It collided with Umbreon, knocking it flat with a burst of black and violet energy. After a moment, it struggled to its feet. It wasn’t ready to faint yet.

    “Hoping I had it? I’m guessing you’re after my Umbreon. Well, too bad! You can’t have him! Umbreon, use Shadow Wave!” the girl ordered.

    Waves of shadow rapidly pulsed off of its body, hitting Mightyena and knocking her a few feet back. The wolf Pokémon snarled, staying on her paws. She wasn’t going to let a fox push her around. Mightyena straightened and launched another Shadow Ball, hitting it hard enough to send it sprawling across the hay-strewn grass.

    “Oh no! Umbreon, use Shadow End!”

    The Umbreon got up, shaking off its pain, and rammed into Mightyena. Its body was coated in a thicker version of its usual shadowy aura. Mightyena yelped, leaping away in agony. With a bitter snarl of vengeance, she let loose one last Shadow Ball and bayed in triumph when the Umbreon collapsed.

    “Oh no! Umbreon!” the girl cried. “This can’t be happening! You aren’t supposed to lose! The man by the Poké Mart said you couldn’t lose to anything!”

    Mark sighed, grabbing a Poké Ball from his bag. It worried him that these kids were just accepting Pokémon from these strange people. Didn’t these kids know any better? Or were they actually agents of Cipher? He really hoped they were not.

    He tossed the ball, watching it pull the Shadow Umbreon inside without issue. Umbreon was caught as cleanly as Espeon and Raichu had been before it. Putting the Snag Ball into his bag, he turned to question the girl, only to find her gone. He scolded himself for taking his eyes off of her.

    With nothing left to do and the day nearing its end, Mark returned to the Pokémon Center in Viridian City. After fixing some ham and macaroni-and-cheese from downstairs for dinner, he let out all six of his Pokémon so that they could also eat.

    He pulled out his PDA and checked Shadow Umbreon’s stats, which were altered towards Attack, just like the others. It was male, normal Synchronize ability, and was Level 16, like Espeon. He went down quickly too, but his attacks had been insanely fast.

    Dinner went by quickly. Mark returned Salamence since he was much too big for the room. Mightyena settled at the foot of the bed, dozing away. Sparks curled up on the covers, watching his trainer shuffle around before bed.

    Strangely enough, Shadow Raichu was up there with Sparks, though he was already asleep. It made Mark nervous to have the moody Raichu that close to him while he was sleeping. The mouse could wake up and attack him while he was vulnerable…or something. He really hoped that the Raichu wouldn’t.

    Mark looked over to the desk and saw Umbreon curled up beside Espeon underneath it. Mark smiled at that. The two seemed rather close, for how short a time they’d known each other. Even with their hearts closed, they somehow sustained something akin to friendship. Maybe it even ran deeper. Mark couldn’t be sure.

    Hopefully that would make life easier on the two of them.

    After taking the dishes downstairs to be washed by the Pokémon Center staff, Mark climbed into bed, Sparks curled up by his side and Raichu hunkered close to the wall behind the Pikachu. Mark lay there and thought about the three Shadow Pokémon that he now had. His thoughts drifted to Cipher, still such an enigma to him.

    Why did Cipher do this? To rule the world through Pokémon? And who were the trainers who had these Pokémon so far? Servants of Cipher? Or just random kids being used to expand Cipher’s turf?

    Mark fell asleep having the same dream as the night before. It was somehow darker, though. The screams were far more piercing this time. Mark could not escape them, no matter how he tried.

    Perched in his window, unseen and undetected by every inhabitant in the room, was a chunky black creature with glowing red eyes and very sharp teeth that formed a crooked smile on its face. It was the source of the nightmares that Mark was being afflicted with.

    It abruptly turned and leaped from the windowsill, disappearing into the night. It had what it wanted now.

    It was off to tell its master what it had learned about this new Snagger.

 

_Elsewhere on an unknown island…_

 

    The creature, a Shadow Gengar, entered a shadowy room and gave its report. It had gotten everything it was required to gather from the boy named Mark. The boy its master was worried about. The boy known as a Snagger.

    A voice spoke from the darkness, clear and cool.

    “Excellent work, my pet. This should prove useful. This new Snagger, unversed and uncoordinated in his new position, will have far more trouble compared to past Snaggers. Now that we have over four hundred Shadow Pokémon, and soon the Legendaries too, and have left the confined, isolated spaces of Orre, there’s no hope that one child can take down our mighty organization. My quest to rule the world will come to fruition.”

    The Shadow Gengar bowed and left, detecting that its master was through speaking to it. Once it left, laughter echoed throughout the chamber.

    Cipher’s leader was beyond pleased.


End file.
